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Issues list

Failure reading CRAM through SamReaderFactory from an FTP input stream cram
#623 opened May 31, 2016 by cmnbroad
CRAMFileReader query calls throw NPE on non-seekable input streams cram
#426 opened Jan 6, 2016 by cmnbroad
@cmnbroad
CRAM reader allows simultaneous iterators, but with inconsistent state cram
#563 opened Apr 9, 2016 by cmnbroad
CRAMFileReader SAMRecordIterator implementations don't implement/honor assertSorted cram
#547 opened Apr 1, 2016 by cmnbroad
Make CRAMFileReader works with CRAI directly cram
#851 opened Apr 11, 2017 by kamyshova
CRAMIterator.next can throw NoSuchElementException when there are more records bug cram
#367 opened Nov 4, 2015 by cmnbroad
Closure of OutputStream in class CRAMContainerStreamWriter cram
#1092 opened Feb 20, 2018 by fversaci
CRAM NPE when writing using an unindexed fasta reference cram
#1152 opened Jun 19, 2018 by lbergelson
Reading a CRAM using a reference file with no dictionary gives misleading error message bug cram
#998 opened Sep 26, 2017 by cmnbroad
CramComplianceTest: four tests from htslib fail due to SAMRecord mismatch cram
#1189 opened Oct 5, 2018 by jmthibault79
CRAM should validate the SAM header against the reference being used cram
#1244 opened Dec 19, 2018 by cmnbroad
CRAM: better testing of unmapped reads cram
#1236 opened Dec 4, 2018 by jmthibault79
CRAM 2.1 test files have incorrect container block byte sizes cram
#1452 opened Jan 17, 2020 by cmnbroad
CRAM huffman codeword is limited to 32 bits cram
#1465 opened Mar 17, 2020 by cmnbroad
Add CRAM compliance tests against hts-specs test files cram
#1587 opened Dec 20, 2021 by cmnbroad
Add support for reserializing CRAM containers cram
#1606 opened Apr 20, 2022 by cmnbroad
1
@cmnbroad
Factor and rename the CRAM ReferenceSource class cram
#604 opened May 12, 2016 by cmnbroad
1
SAMFileWriterFactory doesn't use getDefaultCRAMReferenceSource bug cram
#472 opened Feb 12, 2016 by cmnbroad
@cmnbroad
1
CRAMFileReader doesn't always honor index caching and memory mapping cram
#535 opened Mar 22, 2016 by cmnbroad
1
Figure out there is a bug in BAMIndexMetaData.recordMetaData cram discussion
#401 opened Dec 2, 2015 by lbergelson
1
SequenceUtil.calculateMdAndNmTags does not match other methods cram
#329 opened Sep 23, 2015 by mattsooknah
1
Error executing two sequential SamReader.queryOverlapping() calls for a CRAM File bug cram
#918 opened Jun 26, 2017 by skashin
1
*N cigar op and CRAM slice headers cram
#1088 opened Feb 15, 2018 by jkbonfield
1
CRAM header (and thus md5) varies depending on location of the file when it was created. cram
#1068 opened Jan 11, 2018 by cmnbroad
1
CRAM: Interaction between APDelta and Multi-Reference Slices cram
#1218 opened Nov 1, 2018 by jmthibault79
@jmthibault79
1
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